An increment of diversity method for cell state trajectory inference of time-series scRNA-seq data
Bibliographic record
Abstract
The increasing emergence of the time-series single-cell RNA sequencing (scRNA-seq) data, inferring developmental trajectory by connecting transcriptome similar cell states (i.e., cell types or clusters) has become a major challenge. Most existing computational methods are designed for individual cells and do not take into account the available time series information. We present IDTI based on the Increment of Diversity for Trajectory Inference, which combines time series information and the minimum increment of diversity method to infer cell state trajectory of time-series scRNA-seq data. We apply IDTI to simulated and three real diverse tissue development datasets, and compare it with six other commonly used trajectory inference methods in terms of topology similarity and branching accuracy. The results have shown that the IDTI method accurately constructs the cell state trajectory without the requirement of starting cells. In the performance test, we further demonstrate that IDTI has the advantages of high accuracy and strong robustness.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.003 | 0.011 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.001 | 0.003 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".